[adegenet-forum] DAPC a priori grouping and find.clusters

[Rita Castilho]

Hi,

I am trying to get two DAPCs done:
1. a DAPC1 that displays the a priori established groups (in this case a 
complex of 5 nominal species) and
2. a DAPC2 that displays the genetic gorups, with no a priori 
determination= K clusters

I have produced two scatter plots for these two DAPCs which are 
attached. The first graph (DAPC1) seems to have a y-axis clear division, 
and I was expecting that DAPC2 would display that. But DAPC2 shows a 
horizontal grouping.

Maybe my scripts are not correct. Does anyone can comment if the code is 
correct, or am I making some very basic mistakes?

Many thanks,
Rita



The coding I am using is the following:

data.gp <- read.genepop('infile.gen')
#perform temporary DAPC
dapc <- dapc(data.gp, pop=NULL, n.pca=NULL, n.da=NULL)
a=optim.a.score(dapc, n.pca = 1:ncol(dapc$tab), smart=TRUE, n=10, 
plot=TRUE, n.sim=100, n.da=length(levels(dapc$grp)))
##perform DAPC based on species
dapc.species <- dapc(data.gp, pop=NULL, n.pca=a$best, n.da=NULL, 
scale=FALSE, truenames=FALSE, all.contrib=TRUE)
<<<<<<<<<<<<GRAPH ON THE LEFT>>>>>>>>>>>>>>

#FIND CLUSTERS##################################
clusters <-  find.clusters(data.gp, 
choose.n.clust=TRUE,criterion=c("diffNgroup"), 
n.pca=a$best,n.clust=NULL, stat='BIC', max.n.clust=10)
dapc.clusters<- dapc(data.gp, grp=clusters$grp, n.pca=a$best)
<<<<<<<<<<<<GRAPH ON THE RIGHT>>>>>>>>>>>>>>


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